A series of experiments has been performed to assess some new applications of parallel electron energy-loss spectroscopy in the field-emission STEM. In an application of high-dose analysis of macromolecular assemblies, preliminary data have been obtained from neurofilament HMW subunits in order to determine the number of phosphorylation sites on the molecule; it is believed that there are as many as 20 to 30 phosphates per subunit. Measurements have been made to determine the relative sensitivities of EELS and EDXS for elemental microanalysis of small numbers of atoms bound to biological structures in the STEM, and results indicate that EELS should be favorable for detection of sodium, in addition to phosphorus and calcium. In another application, a study has been performed to determine if EELS can be used to measure the precise thickness of protein crystals, as required for three-dimensional structure determination by electron crystallography. Further progress has also been made in the development of EELS spectrum-imaging techniques, including the extraction of difference spectra from specific features in the spectrum-image.